Adenylyl cyclases (ACs) catalyze the conversion of ATP into the second messenger cAMP and play a key role in signal transduction. In a recent study (Mol Pharmacol 70: 878 -886, 2006), we reported that 2Ј,3Ј-O-(2,4,6-trinitrophenyl)-substituted nucleoside 5Ј-triphosphates (TNP-NTPs) are potent inhibitors (K i values in the 10 nM range) of the purified catalytic subunits VC1 and IIC2 of membranous AC (mAC). The crystal structure of VC1:IIC2 in complex with TNP-ATP revealed that the nucleotide binds to the catalytic site with the TNP-group projecting into a hydrophobic pocket. The aims of this study were to analyze the interaction of TNP-nucleotides with VC1:IIC2 by fluorescence spectroscopy and to analyze inhibition of mAC isoforms, soluble AC (sAC), soluble guanylyl cyclase (sGC), and G-proteins by TNP-nucleotides. Interaction of VC1:IIC2 with TNP-NDPs and TNP-NTPs resulted in large fluorescence increases that were differentially reduced by a water-soluble forskolin analog. TNP-ATP turned out to be the most potent inhibitor for ACV (K i , 3.7 nM) and sGC (K i , 7.3 nM). TNP-UTP was identified as the most potent inhibitor for ACI (K i , 7.1 nM) and ACII (K i , 24 nM). TNP-NTPs inhibited sAC and GTP hydrolysis by G s -and G iproteins only with low potencies. Molecular modeling revealed that TNP-GTP and TNP-ATP interact very similarly, but not identically, with VC1:IIC2. Collectively, our data show that TNPnucleotides are useful fluorescent probes to monitor conformational changes in VC1:IIC2 and that TNP-NTPs are a promising starting point to develop isoform-selective AC and sGC inhibitors. TNP-ATP is the most potent sGC inhibitor known so far.ACs catalyze the conversion of ATP into the second messenger cAMP and play a key role in signal transduction. In mammals, nine membranous AC isoforms (ACI-IX) have been identified (Defer et al., 2000;Sunahara and Taussig, 2002). mACs differ from each other in regulation and tissue expression, and studies with transgenic and gene-knock-out mice have revealed different functions for the various AC isoforms. Most strikingly, ACV is an important AC isoform in the heart (Göttle et al., 2009), and the knock-out of ACV protects mice against heart failure and induces longevity (Yan et al., 2007). Thus, ACV inhibitors may be valuable drugs for the treatment of cardiovascular diseases and ageing (Iwatsubo et al., 2004;Göttle et al., 2009). In addition to mACs, mammals express a structurally distinct sAC that is predominantly found in testis and is important for sperm maturation (Chen et al., 2000). Thus, sAC inhibitors may be promising candidates for male contraceptives (Schlicker et al., 2008). Finally, sGC, catalyzing the conversion of GTP into O-(2,4,6-trinitrophenyl); VC1 and IIC2, the N-and C-terminal catalytic domains from canine type V mAC and rat type II mAC, respectively, expressed as soluble proteins; GTP␥S, guanosine 5Ј-[␥-thio]triphosphate.